Merging changes from old branch into development branch

small changes

Updating visitor architecture to something a bit more modern

Fixed a missing cstdio include

Added some logic to print out a special pair distance as a column in
the stat file.  To use this feature, use taggedAtomPair = "0, 10" and
printTaggedPairDistance = "true" in the md file.  Then, the distance
between integrableObjects 0 and 10 will be computed and printed in
the stat file on each statWrite.

Committing changes made to AtomVisitor to render xyz2pov scenes

Support for printPosOnly in Dump2XYZ.

fixed a build problem...  GB_12b_ratio no longer exists (replaced with BG_l).

testing GB, removing CM drift in Langevin Dynamics, fixing a memory
leak, adding a visitor

adding a gay-berne switch to Dump2XYZ

End of the Link --> List
Return of the Oject-Oriented
replace yacc/lex parser with antlr parser

adding AtomNameVisitor

Couple of changes for TAP water.  Need to parametrize.

fixed the wrapping

adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into
ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;

fix compilation problem for g++ 3.4

adding LipidTransVisitor, GofXyz is working now

IgnoreVisitor and XYZVisitor now use selection library

moved Package variable into subdirectory makefiles to speed up
the building process

merging new_design branch into OOPSE-2.0

replace old GebericData with  new GenericData

change Makefile to relative path

Import of OOPSE v. 2.0